+Open data
-Basic information
Entry | Database: PDB / ID: 7ar9 | ||||||
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Title | Cryo-EM structure of Polytomella Complex-I (membrane arm) | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Complex-I | ||||||
Function / homology | Chem-8Q1 / CARDIOLIPIN / Chem-PC7 / PHOSPHATIDYLETHANOLAMINE Function and homology information | ||||||
Biological species | Polytomella sp. Pringsheim 198.80 (plant) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
Authors | Klusch, N. / Kuehlbrandt, W. / Yildiz, O. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Plant Cell / Year: 2021 Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I. Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun / Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ar9.cif.gz | 936.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ar9.ent.gz | 788.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ar9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ar9_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7ar9_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7ar9_validation.xml.gz | 161.4 KB | Display | |
Data in CIF | 7ar9_validation.cif.gz | 236.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/7ar9 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/7ar9 | HTTPS FTP |
-Related structure data
Related structure data | 11877MC 7aqqC 7aqrC 7aqwC 7ar7C 7ar8C 7arbC 7arcC 7ardC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 33 types, 33 molecules AHJKLMNOTXYZabcdefghijklmnopst...
-Protein/peptide , 2 types, 2 molecules uw
#31: Protein/peptide | Mass: 4273.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) |
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#32: Protein/peptide | Mass: 3507.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Polytomella sp. Pringsheim 198.80 (plant) |
-Non-polymers , 5 types, 384 molecules
#36: Chemical | ChemComp-PC7 / ( #37: Chemical | ChemComp-PTY / #38: Chemical | ChemComp-CDL / #39: Chemical | ChemComp-8Q1 / | #40: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Polytomella complex I - Membrane arm / Type: COMPLEX / Entity ID: #1-#35 / Source: NATURAL |
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Source (natural) | Organism: Polytomella sp. Pringsheim 198.80 (plant) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42350 / Symmetry type: POINT |